Functional Enrichment Analysis | Tool: gprofileR.

net_dir = "/pastel/projects/speakeasy_dlpfc/SpeakEasy_singlenuclei/2nd_pass/snakemake-sn/results/"

macro_type = params$cell_type #macro_structure. It can be cell_type, metabolites, region of the brain. 
message(paste0("Cluster: ", macro_type))
## Cluster: opc

Enrichment Level 03

We removed the clusters with < 30 nodes for downstream analysis.

modules_file = read.table(paste0(net_dir, macro_type, "/geneBycluster.txt"), header = T)
modules_file = modules_file[, c("gene_name", "cluster_lv3")]
modules_file$module_clusters = paste0("m", modules_file$cluster_lv3)
modules_file$cluster_lv3 = NULL
colnames(modules_file) = c("symbol", "module_clusters") #only the sn was with gene_name instead of symbol

modules_size = as.data.frame(table(modules_file$module_clusters))
colnames(modules_size) = c("module", "n_nodes")
createDT(modules_size)

Module enrichment L3

Module m35

Module m23

Module m6

Module m9

Module m31

Module m22

Module m2

Module m3

Module m5

Module m24

Module m38

Module m26

Module m34

Module m10

Module m28

Module m40

Module m44

Module m30

Module m29

Module m1

Module m45

Module m39

Module m37

Module m27

Module m7

Module m32

Module m36

Module m11

Session info

sessionInfo()

R version 4.1.2 (2021-11-01) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Stream 8

Matrix products: default BLAS/LAPACK: /usr/lib64/libopenblasp-r0.3.15.so

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] DT_0.20 plotly_4.10.0 knitr_1.37 gprofiler2_0.2.1 ggeasy_0.1.3 readxl_1.3.1 kableExtra_1.3.4 R.matlab_3.6.2 forcats_0.5.1 stringr_1.4.0
[11] dplyr_1.0.8 purrr_0.3.4 readr_2.1.2 tidyr_1.2.0 tibble_3.1.6 tidyverse_1.3.1 limma_3.50.1 ggfortify_0.4.14 ggplot2_3.3.5

loaded via a namespace (and not attached): [1] bitops_1.0-7 fs_1.5.2 lubridate_1.8.0 webshot_0.5.2 RColorBrewer_1.1-2 httr_1.4.2 tools_4.1.2 backports_1.4.1 bslib_0.3.1
[10] utf8_1.2.2 R6_2.5.1 vipor_0.4.5 DBI_1.1.2 lazyeval_0.2.2 colorspace_2.0-3 withr_2.4.3 tidyselect_1.1.2 gridExtra_2.3
[19] compiler_4.1.2 cli_3.2.0 rvest_1.0.2 xml2_1.3.3 sass_0.4.0 scales_1.1.1 systemfonts_1.0.4 digest_0.6.29 rmarkdown_2.11
[28] svglite_2.1.0 R.utils_2.11.0 pkgconfig_2.0.3 htmltools_0.5.2 dbplyr_2.1.1 fastmap_1.1.0 htmlwidgets_1.5.4 rlang_1.0.1 rstudioapi_0.13
[37] shiny_1.7.1 jquerylib_0.1.4 generics_0.1.2 jsonlite_1.7.3 crosstalk_1.2.0 R.oo_1.24.0 RCurl_1.98-1.6 magrittr_2.0.2 Rcpp_1.0.8
[46] ggbeeswarm_0.6.0 munsell_0.5.0 fansi_1.0.2 lifecycle_1.0.1 R.methodsS3_1.8.1 stringi_1.7.6 yaml_2.3.5 grid_4.1.2 promises_1.2.0.1
[55] crayon_1.5.0 haven_2.4.3 hms_1.1.1 pillar_1.7.0 reprex_2.0.1 glue_1.6.1 evaluate_0.15 data.table_1.14.2 modelr_0.1.8
[64] httpuv_1.6.5 vctrs_0.3.8 tzdb_0.2.0 cellranger_1.1.0 gtable_0.3.0 assertthat_0.2.1 xfun_0.29 mime_0.12 xtable_1.8-4
[73] broom_0.7.12 later_1.3.0 viridisLite_0.4.0 pheatmap_1.0.12 beeswarm_0.4.0 ellipsis_0.3.2